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1.
Curr Microbiol ; 81(8): 247, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38951210

ABSTRACT

Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.


Subject(s)
Genome, Bacterial , Stenotrophomonas , Zea mays , Zea mays/microbiology , Stenotrophomonas/genetics , Stenotrophomonas/metabolism , Biotechnology , Base Composition , Plant Roots/microbiology , Soil Microbiology , Agriculture , Phylogeny , Multigene Family
2.
Gene ; 927: 148669, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38866259

ABSTRACT

Bacillus species are extensively documented as plant growth-promoting rhizobacteria, contributing significantly to the enhancement of soil fertility, nutrient recycling, and the control of phytopathogens. Utilizing them as biocontrol agents represents an environmentally friendly strategy, particularly within the rhizospheric community. This study presents the comprehensive genome sequences of three B. velezensis strains (LGMB12, LGMB319, and LGMB426) which were previously isolated from root samples of maize (Zea mays L.), along with a type strain FZB42. The research assesses the capability of the three strains for antagonizing fungi, specifically Fusarium graminearum, Fusarium verticillioides, Colletotrichum graminicola, and Stenocarpella sp. In paired cultures involving maize fungi, treatments containing bacteria B. velezensis exhibited statistically significant differences compared to both negative and positive treatments in terms of antagonism. Furthermore, genome mining techniques were employed to explore their inherent antagonistic potential. The assembly revealed that strains LGMB12, LGMB319, LGMB426, and FZB42 exhibit genome sizes of 4,187,541 bp, 4,244,954 bp, 3,976,537 bp, and 3,990,518 respectively. Their respective G + C content stands at 46.42 %, 46.50 %, 46.51 %, and 46.38 %. Moreover, the genomes present multiple gene clusters responsible for the synthesis of secondary metabolites and carbohydrate-active enzymes (CAZymes). These clusters highlight a diverse array of antibacterial and antifungal properties, complemented by numerous plant growth-promoting genes. These results highlight the potential of B. velezensis LGMB12, LGMB319, and LGMB426 strains as biocontrol and plant growth promotion agents, being promising candidates for further studies in agricultural production, including field trials.

3.
Arch Microbiol ; 205(9): 325, 2023 Sep 02.
Article in English | MEDLINE | ID: mdl-37659972

ABSTRACT

Common bean is considered a legume of great socioeconomic importance, capable of establishing symbioses with a wide variety of rhizobial species. However, the legume has also been recognized for its low efficiency in fixing atmospheric nitrogen. Brazil is a hotspot of biodiversity, and in a previous study, we identified 13 strains isolated from common bean (Phaseolus vulgaris) nodules in three biomes of Mato Grosso do Sul state, central-western Brazil, that might represent new phylogenetic groups, deserving further polyphasic characterization. The phylogenetic tree of the 16S rRNA gene split the 13 strains into two large clades, seven in the R. etli and six in the R. tropici clade. The MLSA with four housekeeping genes (glnII, gyrB, recA, and rpoA) confirmed the phylogenetic allocation. Genomic comparisons indicated eight strains in five putative new species and the remaining five as R. phaseoli. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparing the putative new species and the closest neighbors ranged from 81.84 to 92.50% and 24.0 to 50.7%, respectively. Other phenotypic, genotypic, and symbiotic features were evaluated. Interestingly, some strains of both R. etli and R. tropici clades lost their nodulation capacity. The data support the description of the new species Rhizobium cerradonense sp. nov. (CNPSo 3464T), Rhizobium atlanticum sp. nov. (CNPSo 3490T), Rhizobium aureum sp. nov. (CNPSo 3968T), Rhizobium pantanalense sp. nov. (CNPSo 4039T), and Rhizobium centroccidentale sp. nov. (CNPSo 4062T).


Subject(s)
Phaseolus , Rhizobium , Brazil , Rhizobium/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Vegetables , DNA
4.
Microbiol Resour Announc ; 12(9): e0047223, 2023 Sep 19.
Article in English | MEDLINE | ID: mdl-37540013

ABSTRACT

The genome sequences of two nitrogen-fixing type strains of the Rhizobium tropici group were obtained: Rhizobium calliandrae CCGE524T and R. mayense CCGE526T. Genomic analyses confirmed their taxonomic position and identified three complete sequences of the repABC genes, indicative of three plasmids, one of them carrying symbiotic genes.

5.
Microbiol Resour Announc ; 12(6): e0018523, 2023 Jun 20.
Article in English | MEDLINE | ID: mdl-37219446

ABSTRACT

The genomes of five elite strains identified as growth promoters of lowland rice (Oryza sativa L.) in Brazil were sequenced. They ranged in size from 3,695,387 bp to 5,682,101 bp, encompassing genes of saprophytic ability and stress tolerance. Genome taxonomy enabled their classification as Priestia megaterium, Bacillus altitudinis, and three putative new species of Pseudomonas, Lysinibacillus, and Agrobacterium.

6.
Int J Mol Sci ; 23(19)2022 Oct 10.
Article in English | MEDLINE | ID: mdl-36233333

ABSTRACT

Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N2, and a major example relies on the high contribution associated with the soybean (Glycine max), contrasting with the low rates reported with the common bean (Phaseolus vulgaris) crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances. In this study, three treatments evaluated in non-sterile soil conditions were investigated in both legumes: (i) non-inoculated control; (ii) inoculated with host-compatible rhizobia; and (iii) co-inoculated with host-compatible rhizobia and Azospirillum brasilense. In the more efficient and specific symbiosis with soybean, Bradyrhizobium presented a high abundance in nodules, with further increases with inoculation. Contrarily, the abundance of the main Rhizobium symbiont was lower in common bean nodules and did not increase with inoculation, which may explain the often-reported lack of response of this legume to inoculation with elite strains. Co-inoculation with Azospirillum decreased the abundance of the host-compatible rhizobia in nodules, probably because of competitiveness among the species at the rhizosphere, but increased in root microbiomes. The results showed that several other bacteria compose the nodule microbiomes of both legumes, including nitrogen-fixing, growth-promoters, and biocontrol agents, whose contribution to plant growth deserves further investigation. Several genera of bacteria were detected in root microbiomes, and this microbial community might contribute to plant growth through a variety of microbial processes. However, massive inoculation with elite strains should be better investigated, as it may affect the root microbiome, verified by both relative abundance and diversity indices, that might impact the contribution of microbial processes to plant growth.


Subject(s)
Microbiota , Phaseolus , Rhizobium , Fertilizers , Nitrogen , Nitrogen Fixation , Phaseolus/microbiology , Plant Roots/microbiology , Rhizobium/physiology , Root Nodules, Plant/microbiology , Soil , Glycine max/microbiology , Symbiosis
7.
Microb Genom ; 8(4)2022 04.
Article in English | MEDLINE | ID: mdl-35438622

ABSTRACT

Soybean is the most important legume cropped worldwide and can highly benefit from the biological nitrogen fixation (BNF) process. Brazil is recognized for its leadership in the use of inoculants and two strains, Bradyrhizobium japonicum CPAC 15 (=SEMIA 5079) and Bradyrhizobium diazoefficiens CPAC 7 (=SEMIA 5080) compose the majority of the 70 million doses of soybean inoculants commercialized yearly in the country. We studied a collection of natural variants of these two strains, differing in properties of competitiveness and efficiency of BNF. We sequenced the genomes of the parental strain SEMIA 566 of B. japonicum, of three natural variants of this strain (S 204, S 340 and S 370), and compared with another variant of this group, strain CPAC 15. We also sequenced the genome of the parental strain SEMIA 586 of B. diazoefficiens, of three natural variants of this strain (CPAC 390, CPAC 392 and CPAC 394) and compared with the genome of another natural variant, strain CPAC 7. As the main genes responsible for nodulation (nod, noe, nol) and BNF (nif, fix) in soybean Bradyrhizobium are located in symbiotic islands, our objective was to identify genetic variations located in this region, including single nucleotide polymorphisms (SNPs) and insertions and deletions (indels), that could be potentially related to their different symbiotic phenotypes. We detected 44 genetic variations in the B. japonicum strains and three in B. diazoefficiens. As the B. japonicum strains have gone through a longer period of adaptation to the soil, the higher number of genetic variations could be explained by survival strategies under the harsh environmental conditions of the Brazilian Cerrado biome. Genetic variations were detected in genes enconding proteins such as a dephospho-CoA kinase, related to the CoA biosynthesis; a glucosamine-fructose-6-phosphate aminotransferase, key regulator of the hexosamine biosynthetic pathway; a LysR family transcriptional regulator related to nodulation genes; and NifE and NifS proteins, directly related to the BNF process. We suggest potential genetic variations related to differences in the symbiotic phenotypes.


Subject(s)
Bradyrhizobium , Fabaceae , Bradyrhizobium/genetics , Genetic Variation , Nitrogen Fixation/genetics , Glycine max
8.
Braz J Microbiol ; 53(1): 267-280, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34984661

ABSTRACT

The use of inoculants carrying diazotrophic and other plant growth-promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as "on farm" production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L. Merrill.) and Azospirillum brasilense for corn (Zea mays L.) or co-inoculation in soybean. The objective was to assess the microbiological quality of such inoculants concerning the target microorganisms and contaminants. In the laboratory, 18 samples taken in five states were serial diluted and spread on culture media for obtaining pure and morphologically distinct colonies of bacteria, totaling 85 isolates. Molecular analysis based on partial sequencing of the 16S rRNA gene revealed 25 genera of which 44% harbor species potentially pathogenic to humans; only one of the isolates was identified as Azospirillum brasilense, whereas no isolate was identified as Bradyrhizobium. Among 34 isolates belonging to genera harboring species potentially pathogenic to humans, 12 had no resistance to antibiotics, six presented intrinsic resistance, and 18 presented non-intrinsic resistance to at least one antibiotic. One of the samples analyzed with a shotgun-based metagenomics approach to check for the microbial diversity showed several genera of microorganisms, mainly Acetobacter (~ 32% of sequences) but not the target microorganism. The samples of inoculants produced on farm were highly contaminated with non-target microorganisms, some of them carrying multiple resistances to antibiotics.


Subject(s)
Azospirillum brasilense , Azospirillum , Bradyrhizobium , Azospirillum/genetics , Azospirillum brasilense/genetics , Bradyrhizobium/genetics , Farms , Humans , Plant Roots/microbiology , RNA, Ribosomal, 16S/genetics , Glycine max/microbiology
10.
ACS Appl Mater Interfaces ; 13(3): 4605-4617, 2021 Jan 27.
Article in English | MEDLINE | ID: mdl-33443996

ABSTRACT

The magnetic properties and ozone (O3) gas-sensing activity of zinc ferrite (ZnFe2O4) nanoparticles (NPs) were discussed by the combination of the results acquired by experimental procedures and density functional theory simulations. The ZnFe2O4 NPs were synthesized via the microwave-assisted hydrothermal method by varying the reaction time in order to obtain ZnFe2O4 NPs with different exposed surfaces and evaluate the influence on its properties. Regardless of the reaction time employed in the synthesis, the zero-field-cooled and field-cooled magnetization measurements showed superparamagnetic ZnFe2O4 NPs with an average blocking temperature of 12 K. The (100), (110), (111), and (311) surfaces were computationally modeled, displaying the different undercoordinated surfaces. The good sensing activity of ZnFe2O4 NPs was discussed in relation to the presence of the (110) surface, which exhibited low (-0.69 eV) adsorption enthalpy, promoting reversibility and preventing the saturation of the sensor surface. Finally, the O3 gas-sensing mechanism could be explained based on the conduction changes of the ZnFe2O4 surface and the increase in the height of the electron-depletion layer upon exposure toward the target gas. The results obtained allowed us to propose a mechanism for understanding the relationship between the morphological changes and the magnetic and O3 gas-sensing properties of ZnFe2O4 NPs.

11.
Microbiol Resour Announc ; 10(1)2021 Jan 07.
Article in English | MEDLINE | ID: mdl-33414299

ABSTRACT

Pseudomonas aeruginosa is known for a high adaptive capacity due to the ability to synthesize several compounds that give advantages for competing with other microorganisms in the environment. The LV strain synthesizes bioactive compounds, mainly by secondary metabolism, with antitumor and antimicrobial activities against microbial pathogens.

12.
Syst Appl Microbiol ; 43(6): 126151, 2020 Nov.
Article in English | MEDLINE | ID: mdl-33171385

ABSTRACT

Bacteria belonging to the genus Paraburkholderia are capable of establishing symbiotic relationships with plants belonging to the Fabaceae (=Leguminosae) family and fixing the atmospheric nitrogen in specialized structures in the roots called nodules, in a process known as biological nitrogen fixation (BNF). In the nodulation and BNF processes several bacterial symbiotic genes are involved, but the relations between symbiotic, core genes and host specificity are still poorly studied and understood in Paraburkholderia. In this study, eight strains of nodulating nitrogen-fixing Paraburkholderia isolated in Brazil, together with described species and other reference strains were used to infer the relatedness between core (16S rDNA, recA) and symbiotic (nod, nif, fix) genes. The diversity of genes involved in the nodulation (nodAC) and nitrogen fixation (nifH) abilities was investigated. Only two groups, one containing three Paraburkholderia species symbionts of Mimosa, and another one with P. ribeironis strains presented similar phylogenetic patterns in the analysis of core and symbiotic genes. In three other groups events of horizontal gene transfer of symbiotic genes were detected. Paraburkholderia strains with available genomes were used in the complementary analysis of nifHDK and fixABC and confirmed well-defined phylogenetic positions of symbiotic genes. In all analyses of nod, nif and fix genes the strains were distributed into five clades with high bootstrap support, allowing the proposal of five symbiovars in nodulating nitrogen-fixing Paraburkholderia, designated as mimosae, africana, tropicalis, atlantica and piptadeniae. Phylogenetic inferences within each symbiovar are discussed.


Subject(s)
Burkholderiaceae/classification , Fabaceae/microbiology , Phylogeny , Root Nodules, Plant/microbiology , Bacterial Typing Techniques , Brazil , Burkholderiaceae/isolation & purification , DNA, Bacterial/genetics , Genes, Bacterial , Mimosa/microbiology , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis
13.
Int J Syst Evol Microbiol ; 70(7): 4233-4244, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32568030

ABSTRACT

Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.


Subject(s)
Agrobacterium/classification , Glycine max/microbiology , Phaseolus/microbiology , Phylogeny , Root Nodules, Plant/microbiology , Agrobacterium/isolation & purification , Bacterial Typing Techniques , Base Composition , Brazil , DNA, Bacterial/genetics , Ecuador , Genes, Bacterial , Mexico , Mozambique , Nitrogen Fixation , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
14.
ACS Omega ; 5(17): 10052-10067, 2020 May 05.
Article in English | MEDLINE | ID: mdl-32391493

ABSTRACT

Novel magnetic metals and metal oxides that use both the spin and charge of an electron offer exciting technological applications. Their discovery could boost research on functional nanoscale materials. Here, for the first time, we report the magnetization of α-Ag2WO4 under electron beam and femtosecond laser irradiation. The formation and growth of silver oxides (AgO, Ag2O, and Ag3O4) and Ag nanofilaments can be observed on the surface of α-Ag2WO4 crystals. These features were also present in the composition of an extruded material and could open new avenues for surface magnetism studies. In order to understand these results, we used first-principles density functional theory calculations. This allowed us to investigate several potential scenarios for controlling magnetic properties. The effect of electron addition on the crystalline structures of α-Ag2WO4, Ag3O4, Ag2O, and AgO has been analyzed in detail. The creation of Ag and O vacancies on these compounds was also analyzed. Based on structural and electronic changes at the local coordination site of Ag, a mechanism was proposed. The mechanism illustrates the processes responsible for the formation and growth of metallic Ag and the magnetic response to electron beam irradiation.

15.
Arch Microbiol ; 202(6): 1369-1380, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32166359

ABSTRACT

A polyphasic study was conducted with 11 strains trapped by Mimosa pudica and Phaseolus vulgaris grown in soils of the Brazilian Atlantic Forest. In the phylogenetic analysis of the 16S rRNA gene, one clade of strains (Psp1) showed higher similarity with Paraburkholderia piptadeniae STM7183T (99.6%), whereas the second (Psp6) was closely related to Paraburkholderia tuberum STM678T (99%). An MLSA (multilocus sequence analysis) with four (recA, gyrB, trpB and gltB) housekeeping genes placed both Psp1 and Psp6 strains in new clades, and BOX-PCR profiles indicated high intraspecific genetic diversity within each clade. Values of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) of the whole genome sequences were of 56.9 and 94.4% between the Psp1 strain CNPSo 3157T and P. piptadeniae; and of 49.7% and 92.7% between the Psp6 strain CNPSo 3155T and P. tuberum, below the threshold for species delimitation. In the nodC analysis, Psp1 strains clustered together with P. piptadeniae, while Psp6 did not group with any symbiotic Paraburkholderia. Other phenotypic, genotypic and symbiotic properties were evaluated. The polyphasic analysis supports that the strains represent two novel species, for which the names Paraburkholderia franconis sp. nov. with type strain CNPSo 3157T (= ABIP 241, = LMG 31644) and Paraburkholderia atlantica sp. nov. with type strain CNPSo 3155T (= ABIP 236, = LMG 31643) are proposed.


Subject(s)
Burkholderiaceae/classification , Burkholderiaceae/isolation & purification , Mimosa/microbiology , Nitrogen-Fixing Bacteria/isolation & purification , Phaseolus/microbiology , Base Composition/genetics , Brazil , Burkholderiaceae/genetics , DNA, Bacterial/genetics , Forests , Genes, Essential/genetics , Multilocus Sequence Typing , Nitrogen , Nitrogen-Fixing Bacteria/classification , Nitrogen-Fixing Bacteria/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Soil , Soil Microbiology
16.
Front Microbiol ; 11: 618415, 2020.
Article in English | MEDLINE | ID: mdl-33519779

ABSTRACT

The main objective of this study was to evaluate Bacillus velezensis strain CMRP 4490 regarding its ability to inhibit soil-borne plant pathogens and to increase plant growth. The study included evaluation of in vitro antifungal control, sequencing the bacterial genome, mining genes responsible for the synthesis of secondary metabolites, root colonization ability, and greenhouse studies for the assessment of plant growth-promoting ability. The strain was obtained from soil samples in the north of Paraná in Brazil and was classified as a B. velezensis, which is considered a promising biological control agent. In vitro assay showed that B. velezensis CMRP 4490 presented antagonistic activity against Sclerotinia sclerotiorum, Macrophomina phaseolina, Botrytis cinerea, and Rhizoctonia solani with a mycelial growth inhibition of approximately 60%, without any significant difference among them. To well understand this strain and to validate its effect on growth-promoting rhizobacteria, it was decided to explore its genetic content through genome sequencing, in vitro, and greenhouse studies. The genome of CMRP 4490 was estimated at 3,996,396 bp with a GC content of 46.4% and presents 4,042 coding DNA sequences. Biosynthetic gene clusters related to the synthesis of molecules with antifungal activity were found in the genome. Genes linked to the regulation/formation of biofilms, motility, and important properties for rhizospheric colonization were also found in the genome. Application of CMRP 4490 as a coating film on soybean increased from 55.5 to 64% on germination rates when compared to the control; no differences were observed among treatments for the maize germination. The results indicated that B. velezensis CMRP 4490 could be a potential biocontrol agent with plant growth-promoting ability.

17.
Int J Syst Evol Microbiol ; 69(12): 3863-3877, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31486763

ABSTRACT

The symbioses between legumes and nitrogen-fixing rhizobia make the greatest contribution to the global nitrogen input via the process of biological nitrogen fixation (BNF). Bradyrhizobium stands out as the main genus nodulating basal Caesalpinioideae. We performed a polyphasic study with 11 strains isolated from root nodules of Chamaecristafasciculata, an annual multi-functional native legume of the USA. In the 16S rRNA gene phylogeny the strains were clustered in the Bradyrhizobium japonicumsuperclade. The results of analysis of the intergenic transcribed spacer (ITS) indicated less than 89.9 % similarity to other Bradyrhizobium species. Multilocus sequence analysis (MLSA) with four housekeeping genes (glnII, gyrB, recA and rpoB) confirmed the new group, sharing less than 95.2 % nucleotide identity with other species. The MLSA with 10 housekeeping genes (atpD, dnaK, gap, glnII, gltA, gyrB, pnp, recA, rpoB and thrC) indicated Bradyrhizobium daqingense as the closest species. Noteworthy, high genetic diversity among the strains was confirmed in the analyses of ITS, MLSA and BOX-PCR. Average nucleotide identity and digital DNA-DNA hybridization values were below the threshold of described Bradyrhizobium species, of 89.7 and 40 %, respectively. In the nifH and nodC phylogenies, the strains were grouped together, but with an indication of horizontal gene transfer, showing higher similarity to Bradyrhizobium arachidis and Bradyrhizobium forestalis. Other phenotypic, genotypic and symbiotic properties were evaluated, and the results altogether support the description of the CNPSo strains as representatives of the new species Bradyrhizobiumfrederickii sp. nov., with CNPSo 3426T (=USDA 10052T=U686T=CL 20T) as the type strain.


Subject(s)
Bradyrhizobium/classification , Chamaecrista/microbiology , Phylogeny , Root Nodules, Plant/microbiology , Bacterial Typing Techniques , Base Composition , Bradyrhizobium/isolation & purification , DNA, Bacterial/genetics , Gene Transfer, Horizontal , Genes, Bacterial , Missouri , Multilocus Sequence Typing , Nebraska , Nitrogen Fixation , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis , Temperature
19.
Int J Syst Evol Microbiol ; 69(11): 3448-3459, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31429819

ABSTRACT

Information about the symbionts of legumes of the Caesalpinioideae subfamily is still limited, and we performed a polyphasic approach with three Bradyrhizobium strains-CNPSo 3448T, CNPSo 3394 and CNPSo 3442-isolated from Chamaecrista fasciculata, a native legume broadly distributed in the USA. In the phylogenetic analysis of both the 16S rRNA gene and the intergenic transcribed spacer, the CNPSo strains were clustered within the Bradyrhizobium japonicumsuperclade. Multilocus sequence analysis with six housekeeping genes-glnII, gyrB, recA, rpoB, atpD and dnaK-indicated that Bradyrhizobium diazoefficiens is the closest species, with 83 % of nucleotide identity. In the genome analyses of CNPSo 3448T, average nucleotide identity and digital DNA-DNA hybridization results confirmed higher similarity with B. diazoefficiens, with values estimated of 93.35 and 51.50 %, respectively, both below the threshold of the same species, confirming that the CNPSo strains represent a new lineage. BOX-PCR profiles indicated high intraspecific genetic diversity between the CNPSo strains. In the analyses of the symbiotic genes nodC and nifH the CNPSo strains were clustered with Bradyrhizobium arachidis, Bradyrhizobium forestalis, Bradyrhizobium cajani, Bradyrhizobium kavangense and Bradyrhizobium vignae, indicating a different phylogenetic history compared to the conserved core genes. Other physiological (C utilization, tolerance to antibiotics and abiotic stresses), chemical (fatty acid profile) and symbiotic (nodulation host range) properties were evaluated and are described. The data from our study support the description of the CNPSo strains as the novel species Bradyrhizobiumniftali sp. nov., with CNPSo 3448T (=USDA 10051T=U687T=CL 40T) designated as the type strain.


Subject(s)
Bradyrhizobium/classification , Chamaecrista/microbiology , Nitrogen Fixation , Phylogeny , Root Nodules, Plant/microbiology , Bacterial Typing Techniques , Base Composition , Bradyrhizobium/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genes, Bacterial , Missouri , Multilocus Sequence Typing , Nitrogen , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis
20.
Arch Microbiol ; 201(10): 1435-1446, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31428824

ABSTRACT

A polyphasic approach was used to infer the phylogenetic position of six nitrogen-fixing symbiotic bacteria isolated from Mimosa gymnas nodules grown in an ecotone between the Brazilian biomes of Atlantic Forest and Cerrado, considered as a hotspot of biodiversity. The 16S rRNA gene phylogeny indicated the highest similarity with Paraburkholderia oxyphila (98.7-98.9%), but similar values were found with other Paraburkholderia species. The multilocus sequence analysis (MLSA) of five (recA, gyrB, trpB, gltB, and atpD) housekeeping genes indicated that the CNPSo strains represent a novel lineage, sharing less than 95.7% of nucleotide identity (NI) with other Paraburkholderia species, being more closely related to P. nodosa. Genome parameters were analyzed for strain CNPSo 3008T, and DNA-DNA hybridization revealed a maximum of 55.9% of DNA-DNA relatedness with P. nodosa, while average nucleotide identity with the two closest species was of 93.84% with P. nodosa and of 87.93% with P. mimosarum, both parameters confirming that the strain represents a new species. In the analysis of the nodulation nodC gene, all CNPSo strains showed the highest similarity with P. nodosa, and nodulation tests indicated host specificity with Mimosa. Other phylogenetic, physiological, and chemotaxonomic properties were evaluated. All data obtained support the description of the novel species Paraburkholderia guartelaensis sp. nov., with CNPSo 3008T (= U13000T = G29.01T) indicated as the type strain.


Subject(s)
Burkholderiaceae/classification , Mimosa/microbiology , Phylogeny , Root Nodules, Plant/microbiology , Base Composition , Brazil , Burkholderiaceae/genetics , Burkholderiaceae/isolation & purification , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Genes, Bacterial/genetics , Multilocus Sequence Typing , Nitrogen Fixation , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species Specificity
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